The Pandoran Incident
by jjenni65
Summary: <html><head></head>During a top-secret Republic Mission, Jedi Aayla Secura and Commander Wolffe are sent to Pandora to destroy Seperatist Outpost in the Unkown Regions.  Because of the secrecy, Aayla survives Order 66 but soon Stormtroopers arrive with Darth Vader.</html>
1. Order 66

"Commander Bly."

"Yes my lord?"

"The time has come, execute Order 66."

"But sir-" cried the clone in shock.

"That is an order, commander." Growled the sinister voice in response to the insubordinate outburst.

"Yes, my lord. It will be done." Bly had a mixture of emotions running through him as he switched off the communication device. He had been skeptical when he received a high-priority transmission from a _separatist_ code. He was going to show it to Aayla Secura when he heard the command it had issued. When he was briefed before the war on Kamino of this possible scenario, he thought it would be easy. That was before he met Aayla. He and his men had formed a tight bond with their charismatic general. As time had passed with no problem Bly and his men had begun to hope this day would not come. It was all in vain, Aayla now had turned traitor and had to die. The fact that just days before she had complimented them as "the bravest soldiers and greatest friends she could hope for."

Bly swore, how could he break it to the men? He switched to the text transmission system in his helmet, only a few of his most trusted officers would have to know before the fact. It also prevented Aayla from finding out what was happening. _She's over by the second AT-TE, we'll meet up there._ He finished the transmission with an empty heart, he couldn't do this to the men; he knew what they were going through.

Sure enough, Aayla was over by the AT-TE, his men were already there. Aayla looked at him and smiled, Bly was glad he had his helmet, as his facial expression would have given them away for sure. She motioned for them to follow and walked into the jungle. They followed, but not on her orders. One of the men had the guts to break the silence, "Where are the captive Jedi being held again?"

It must have been his tone that told her something, Aayla tensed up, Bly took a step back; he didn't want to be ka-bobbed by his friend's lightsaber. "Listen," she whispered, "the forest has gone silent, Bly, do you think it's droids?"

That pushed Bly over the edge, his voice cracked, "No." He really hoped he didn't have to look her in the eye.

"Then what-" she never finished, Bly shot her in the back. She fell forwards. The men began to freak out and shot rapidly at her body on the ground. It wasn't thrashing around. Bly ordered them to stop and they walked back towards the convoy to tell the men the bad news. They were weeping, not able to look back at their betrayed friend. If they had, they would have known it wasn't their friend, but a droid covered with a hologram of her.


	2. Foresight

5 Months Previous…

"Tell me again Senator Organa, why is this necessary?" asked Aayla, skeptically.

"This is a very risky operation here Master Jedi," explained the hologram on board the Republic Battleship _Liberator_, "it is essential that this remains top-secret, we do not want to cause mass-panic, I'm not even sure the Chancellor knows of this operation. If the Separatists do have a stronghold in the Unknown Regions then it is in our best interests to eliminate it before they can launch any surprises."

"And you know of this base because?" she inquired further.

"Just a hunch," Aayla gave him a quizzical glance, "AND we have been picking up droid chatter in sector 789-98-712."

"You realize this could just be another civilization that has progressed as far as we have, senator."

"If it is, then it is critical that we get their support to gain an upper hand in this war."

"But this is not their war senator!" Aayla exclaimed with more emotion than she intended, "We can't make them die for a cause they didn't have any part in!"

"Better we find them, than Grievous or Count Dooku." Said Bail Organa silently.

"I'm sorry senator, I was not thinking clearly. My mind has not been at peace the last few days." She replied quickly. "Please go on."

"We have built an IG-97 droid to take your place so no one gets suspicious. As far as the common clone knows, you are investigating a Separatist presence on Felucia with Commander Bly."  
>"Bly doesn't even know?" she felt bad keeping something from her second-in-command, and close friend.<p>

"Yes, Bly doesn't even know. You'll be back before he's missed you."

"He's not stupid, senator. A droid can't use the force."

"No but we've incorporated a super-magnetizer to its body. It'll be able to send droids flying up to fifty meters."

"I hope you're right senator," responded Aayla, rubbing her chin, "it would be tough to explain _that_ to the senate…"

"Your ship's Nava computer has the coordinates preset. We have sent out drones ahead to plot a safe route a safe distance away from any newly discovered red-dwarves. You will have Commander Wolfe and the 417th to assist you on your expedition. I would observe radio silence after this transmission; we don't want anyone intercepting them."

"It will be hard enough to explain the disappearance of a Jedi Cruiser…"

Bail smiled, "That's just it; this cruiser doesn't exist. Commander Wolfe and the 417th were all reported Missing in Action after the Battle of Salucami." The look on Aayla's face was unforgettable and Bail's smile increased exponentially, "Goodbye Master Jedi." The hologram switched off. Aayla turned to see a clone in purple armor behind her.

"You must be Commander Wolfe."

"Unit CC-374 reporting for duty sir, er ma'am." He stammered. "Sorry, I last served under General Windu, how should I address you?"

"Aayla will be fine." said Aayla, giving him an amused look.

"No, really, how do I address you? I am not your equal."

"But I do hope we can become friends in time Wolfe." She replied.

"Very well General Aayla," he responded with a stiff salute, and quickly changed the subject. "The men are assembled in the main hangar for inspection."

"Let's not make them wait any longer."

The 417th was assembled in 100 ranks 300 abreast; all were at attention as Aayla walked in front of them with Wolfe. "Most impressive…" she said thoughtfully, "All are experienced?"

"Yes general, all of them fought at Salucami."

"Then I have a deep respect for you all, Grievous inflicted much damage on your troops; you are all very brave men. When this war is over, the entire galaxy will recognize you as the few heroes that destroyed the Separatist threat. You all are dismissed, get rest, we'll be at our destination in two days."

"What?" bellowed Wolfe, "You all got mud in your ears? You heard the General, DIS-MISSED!"

The clones snapped to attention, did a fierce salute followed by an unanimous "Oo-ya!" and marched out the hangar doors to their barracks. Aayla turned to Wolfe, "You certainly have fine men here."

"They are my clones General; they are totally obedient to their commanding officer, as I am to you."

"True, that reminds me, I want to know what you wish to do after the war."

"_After_ the war general?" he repeated, completely puzzled, "I don't really know, I suppose whatever you order me to do."

"Don't you have any dreams that you want to fulfill?" Aayla asked, puzzled too.

"You are a Jedi," replied Wolfe hesitantly, "You have dreams too, but you put those behind you to serve the Republic. We clones are that way too, we didn't have a choice, but we don't mind, our mind-set won't allow us to."

A sudden flash of anger went through Aayla's mind; _The Kaminoans are monsters, creating intelligent life simply to use them as tools. These are free-thinking men, not docile service-droids!_ She managed to contain it, "Seems a little unfair, don't you think?"

"I suppose…" thought Wolfe for a moment, "You need not worry about us General, we are happy the way we are, even if it's because of genetic tampering."

That made Aayla even madder.

"Are you alright General?"

Aayla kissed him on the cheek, "Just let it be known that someone in the universe cares for you and your brothers. Now go join your men."

"Yes sir-I mean ma'am-I mean-" stammered Wolfe again, blushing uncontrollably. He put on his helmet and jogged away to be with his men.

Silently Aayla belittled herself, maybe she wasn't meant to be a General. She could not let her emotions control her like that. Yet, she found that she _liked_ kissing him on the cheek-what the hell was she thinking; what would Master Yoda think of this? She smiled at that thought and began the walk back to the bridge.


	3. Contact

Pandora

At 09:17 Coruscant time the _Liberator_ came out of Hyperspace over Pandora. Senator Organa had made extremely precise calculations as to where to send them. Aayla thanked his intelligence; if they had been in Hyperspace for another second they would have flown through the Gas Giant that a forested moon was orbiting. "Commander," she said, not turning from the view screen, "Surface-scan."

"Yes general," saluted Wolffe as he activated the ultra-sonic scan of the surface below.

Hell's Gate

The name said it all; it had been the name for the Human HQ on Pandora. After the battle with the Na'vi, the humans had been forced to land again in the _Valkarie_ Shuttle because they could not find their Interstellar Ship. Gradually peace insured between the Humans and the Na'vi, but it didn't take them long to find out what had happened to the ship.

Na'vi Hunters found pieces of scrap metal that they had seen fall from the sky; some of it was marked with the RDA insignia. The spaceship had been destroyed. By who was discovered the next day when another ship landed on the Landing Pad-after destroying the _Valkarie _so it could land. Out of its belly marched wave after wave of droids, firing like crazy. The humans fought back hard, but bullets could not harm them. AMP Suits lasted a while, until tanks began to emerge from the ship's depths. The droids slowly but surely gained ground until the station's commander, Kendra Midori was forced to surrender.

The Droid General's name was Malcogni; he was a Malcognit Prototype for the Separatist High Command. He was different from other droids in the Separatist Army; he actually _learned_ from his enemies and was programmed in the use of the lightsaber. He sat reclined in the leather chair in the office that had once belonged to Col. Miles Quarich. Even his own droids left him alone, he had a very humanlike personality-and temper, so when a Droid Commander burst into his train of thought he knew it was something really important. This didn't mean he liked it. "What _is _it? Before you speak, remember that you are easily replaceable!"

"I understand Commander," droned the droid, if droids had emotions, this droid had become _very _nervous, "Our sensors have detected a surface-scan of the surface, it appears to be ship-based and is using a Republic Frequency."

Malcogni was silent for a moment, "It seems as though we have a few guests commander," he chuckled, "let's give them a Separatist welcome." He laughed; the droid didn't get it, but wisely decided to join him.

"Contact," Reported the officer manning the scanner, "sector 3-5-01, course set to intercept us…"

"It appears there _is_ intelligent life on this rock general." Smiled Wolffe, Aayla did not return the gesture.

"Something is not right," she said philosophically, "why have they not tried to contact us yet?"

"It's powering up weapons systems general!" shouted the officer louder than intended, "It's a Separatist Battleship!"

"All hands to battle-stations!" ordered Wolffe. Alarms instantly began blaring throughout the ship. Aayla remembered the last time she had been in a space battle; her commanding skills would have killed them all if Anakin Skywalker hadn't shown up to save their butts. She was not about to repeat that.

"Vulture droids inbound." Continued the officer.

"Concentrate on the Battleship," responded Aayla, "We'll take care of the Vulture droids." She immediately left the bridge and used the force to open the shaft doors. There was no elevator, but she wasn't about to let that tiny little detail stop her; she activated her lightsaber and jumped at the fall wall, using her lightsaber to slide down the shaft at a controlled speed. Behind her Wolffe whistled impressed.

When she sensed she had reached the hangar level, she opened the door and back flipped off of the wall through the door, hitting the ground at a sprint. Clones saluted her, quickly opening doors to admit her. When she reached the hangar, most of the fighters had already been launched and R5-D3 was waiting patiently in her Jedi Star fighter. Without breaking a stride she leapt into the cockpit and began takeoff.

The Vulture droids were droids, they had no self-preservation programmed into them; they'd commit suicide if it meant that they could kill a few more of the enemy. That was what made them dangerous. The Separatists had begun to use them as hi-tech missiles. The _Liberator_ was concentrating its fire on the Separatist Battleship but Aayla quickly saw that the _ARC _and _V-wing_ clone fighters were not going to be able to survive much longer against the Vulture droids. There were easily enough Vulture droids to fly into all the clone fighters, destroy the _Liberator_ and still have some left to tell their droid friends about it. However, the Vulture droids were being controlled from the Battleship and if that was destroyed…

Aayla sent a transmission, "Bombardier come in."

"Yes general?" came the response.

"Move your squadron forward; drive the Vulture droids towards their Battleship."

"Right away." Came the response, had Aayla received that order she would have at least asked why her commander wanted her to draw the enemy towards their own ship where she would be a sitting duck; another sign of the Clone's mental alterations.

The droids seemed to have noticed that the enemy was now virtually defenseless, and decided to send bombers off to finish them. In order to do that they would have to lower their shields. Aayla dove at the Separatist hangar, firing her ship's guns, right as their bombers were taking off. One of the bombers was hit, swerved, and they all crashed, their explosives going off at the same time. The hangar shield generators could not withstand the blast and were shut off-permanently.

"All Y-wing bombers," she sent out, "Drop your payloads in the enemy hangar!"

"Yes general," they repeated, all flying towards the hangar. Separatist hangars went all the way through the ship and were wide enough for sixteen bombers to fly in side by side, a design that was about to prove fatal. The sixteen Republic Bomber Pilots were experienced, and all easily managed to fly in without any issues. Once inside, full payloads from the sixteen ships wrecked havoc throughout the ship; the force was strong enough to rip the ship in half as the triumphant heroes flew out the other side. Aayla would personally commemorate every one of those pilots and crew.

The Droid Commander entered Malcogni's office again, this time with bad news. At least Malcogni seemed to be in a good mood then, and the droid wondered how quickly that could change. He made his report and finished saying, "I'm sorry sir, it will not happen again."

Malcogni nodded thoughtfully for a moment, and then decapitated the droid with his lightsaber. "Apology accepted Commander." He pressed a button, "Sergeant!"

The door opened and a battle droid stepped tentatively in, "Yes sir?"

"Tell the troops to prepare for ground assault," the droid bent down towards the headless commander droid, "Leave him," waved Malcogni, "and unless you wish to join him, I would get on with doing as I instructed."

"Roger roger." Said the droid emotionlessly.


	4. Friends

Pandora

"Come here very quickly Ablerider." Instructed Tan Jala, pointing at the sky above, "Bring Jakesully as well." The two Avatars joined him on the tree branch.

"What's up Tan Jala?" replied Rider, sitting next to him. Tan Jala's face changed to one of much confusion.

"What is up?" he inquired, not understanding, "What is up is a message from Eywa." He pointed to the sky where they could distinctly see bright colorful flashes light up the sky. "They sent up a metal ikran up there not long time ago."

"Looks like they found some trouble," said Jake, rubbing his chin thoughtfully, "help may have arrived… or it could be another enemy."

"An enemy of an enemy is a friend." Smiled Tan Jala.

"I hope you're right," replied Jake, "what we really need now is a friend." He was right too; ever since the Battle of Hell's Gate, a ragtag group of human survivors and Na'vi Hunters had been wandering around in the Pandoran Jungle. The droids had not destroyed the new Na'vi Hometree, but it was only a matter of time before the place was swarming with droids. Among the humans were Kendra, Dalton, Conrad, Lyle Wainfleet, and Tom. Among the Na'vi were Beyda'amo, Neytiri, Marali, Amanti, Unipey, and Tsu-tsey. Together, the force of about 300 were Public-Enemy-Number-One for the droids and Malcogni, having sabotaged several of their operations, and were classified as "eliminate-on-sight". The key word was "sight" because the force was never seen out in the open for longer than five seconds. They had been a thorn in Malcogni's side for a long time, and every encounter became harder to survive; Malcogni learned fast for a droid.

"What's going on up here?" asked Kendra, walking up to meet them. The bursts of light were now picking up in frenzy.

"A sign from Eywa," commented Unipey as she strode up to meet them, "we are alone no longer."

"Great," muttered Tsu-tsey cynically, "more Tawtute, I hope they are better than the last few groups…" Kendra raised an eye-brow in his direction.

1,000 yards higher…

The 30 Republic Gunships launched themselves from the _Liberator_ and began to speed towards Hell's Gate. A Nava specialist had trace the Enemy Battleship's flight path to a facility that scans showed was loaded with battle-droids. Now Aayla was gripping the arm hold along with Wolffe and ten other clones in one of the gunships. The doors were open and a clone with a rocket-launcher crouched next to each. _Reminds me of Felucia._ Thought Aayla, admiring the planet's beauty. The target appeared on the horizon and they began to descend.

A group of black objects took to the air in the distance and began to grow larger. Wolffe took looked at the objects closely, using his helmet's magnification to get a better look, "Trouble," he reported, "More Vulture droids inbound."

"Pilot, take us down." Ordered Aayla, "We can not risk our men by attempting a direct assault."

"Yes sir-er general!" the pilot replied with awkwardness displayed previously by Wolffe. Aayla sighed; she wished she didn't have to be the _only_ one issuing commands around. The Gunships dropped like stones; Aayla had to grab the rocket launcher bearing clone to her left so that he didn't fall out.

The clone looked up, "You just saved my life."

"Yes trooper, that's what friends do." She replied, smiling.

The clone only stared back, "Thank you general."

_What monsters have the Kaminoans created?_ She asked herself, shocked by the trooper's monotone. When this war was over, she would personally shut down the Kamino Cloning Facilities for good. Wolffe was looking at her, she was having another moment. She pulled it together just as the pilot reported, "Nearing ground level."

"Look," shouted Conrad, "They are landing." Everyone looked at the clearing where the 30 alien craft were landing; the humans reached for their guns, the Na'vi their bows. They saw 360 men in white armor that covered their entire bodies disembark carrying strange-looking guns. One of the men was wearing armor with purple markings, but the strangest of all was their leader. She was around the height of a human, had blue skin, and two strange tail-like organs that took the place of hair. She was wearing leather-like clothing that covered the required areas, but not much else. She carried a small metal rod in place of a gun and was instructing the men with what looked like rocket-launchers to take positions around them. They weren't quite sure why until they heard it.

"Enemy fighters…" Growled Kendra. The howl grew louder until fifty black shapes flashed overhead. The blue woman gave the signal and the rocket men fired a barrage of rockets after them. Fifty explosions sounded in the distance, none of them returned. Kendra whistled, "…are nothing to these guys."

"Yes," replied Neytiri, "but are many metal demons?" she pointed to a spot of jungle not 400 yards away from the new heroes. There was row after row of battle droids marching their way.

"We have to warn them." Answered Wainfleet, jumping into one of the AMP Suits, "Our new friends are about to save our asses, but first we have to save theirs!" Na'vi jumped onto Direhorses and Ikrans. Humans crawled into AMP Suits and Scorpion Helicopters. The show was about to begin.

"Great shot!" shouted Wolffe enthusiastically clapping clones of the back. _At least they are capable of some emotion._ Smiled Aayla, then, _Northeast!_

"We aren't alone," she interrupted the Clones' jubilation, "movement to the northeast."

"Take defensive positions!" ordered Wolffe, back to his old self instantly. The 300 clones with blasters formed a defensive line with the rocket bearers behind them, all aiming at the rustling foliage. Out walked a woman dressed in a camo-uniform with a mask over her face carrying a primitive-looking gun. They had been told that the atmosphere of the moon contained toxic gases and not to remove their helmets. Aayla was exempt from this because her home world of Ryloth contained similar gases in its atmosphere. Out came more humans, some in metallic exoskeletons. There was the sound of a turbine and Aayla turned to see an ancient flying machine-the helicopter-take to the skies.

Still looking at the sky, she saw brightly colored aerial creatures take flight with humanoid creatures on their backs. Turning back to the jungle, she saw more come out, some on foot, and some on more six-legged domestic creatures. The humanoids carried bows and melee weapons and were easily twice the size of a tall human. They had blue skin and long black hair. They were dressed like she was, except for two, who were wearing clothes similar to the humans and were carrying more of the guns. She saw her men with their blasters raised, taking aim, "Stand down." She ordered and the clones put down their weapons like trained pets. _I have to stop thinking of them like that!_ She belittled herself, _They are people too!_ She looked up to see that the humans had paused, confused expressions on their faces.

"You speak English." Gasped the lead woman. Everyone on both sides took a step back in surprise. This planet may have been a long-lost Republic Colony and "English" was an adaptation of Basic. "You seem to be the enemy of our enemy, so you should be a friend.

"We would hope to be." Replied Aayla. She was about to continue when the woman stopped her.

"Speaking of enemies, there is a lot of them attempting to flank you as we speak." She added nonchalantly as if it meant nothing to her.

"Oh really?" replied Aayla heightening her senses and sure enough, she detected about a thousand battle droids moving to the southeast. She mentally told her troops this; they nodded in acknowledgement and took cover behind the gunships. The humans eyed her quizzically as Aayla added, "You may have also overlooked something else."

It was the woman's turn to appear surprised, "And what would that be?"

"While you were paying attention to their distraction, a larger group is moving up from behind you." The woman cursed and the contingent began fidgeting with their weapons nervously, "But don't worry," assured Aayla, "I have full confidence in my men destroying the first group, I will deal with the second."

"You are indeed a brave woman," said one of the blue people, "but how will you fight without a weapon. As if on cue, droids emerged from both sides of the clearing and instantly began firing.

"Who said I don't have a weapon?" asked Aayla, raising an eyebrow teasingly and sprinted at the droids while igniting her lightsaber. The humans and blue men were stunned by the appearance of the beautiful blue shaft of deadly light. They had a few more surprises coming.

The droids may have been mindless, but were not idiotic; they quickly realized that their biggest threat was not clones, Na'vi, or human, but the lone Twi'lek Jedi charging at them. Their weapons were useless; every shot sent her way was deflected back at them. She was quickly in the middle of their ranks, butchering everything in her blue saber's path. She also struck with her hands, feet and head, physically tearing them apart as well. She also used the force to deal with droids too far away to hit with the lightsaber. Most of the Na'vi and Humans joined her, driving them back, but some stayed with the clones, lead bravely by Wolffe, who were ripping apart droids left and right. In less than ten minutes, the remains of all three thousand battle droids lay in heaps on the deck. The clones had sustained minimal casualties, most being bruises, and the humans and Na'vi sustained none.

"That was fun." Replied the woman, kicking a droid head, "What's the plan?"


	5. Old Friends

Five months later, Coruscant

"You summoned me sir?" asked the mechical voice.

"You seem to have made progress with the Physical Therapy Lord Vader," answered the Emperor's raspy sinister voice, "are you ready for your next assignment?"

"Yes, my master. Kenobi thought he could kill me, he has made a huge underestimate of my skills."

"_Over_statement, Lord Vader." Corrected the Emperor, "The fact remains that you are weak and failed to complete my assignment."

"I will not fail you again, master." Answered Vader respectfully, "What is my next assignment?"

"Why don't you ask your friend?" smiled Papaltine sinisterly, "At least _he _still remembers you. Bring him in."

The doors slid open and in marched two stormtroopers, and in between them was a beaten, Jar-jar Binks. Vader recognized him instantly, but showed nothing, "Stand up." Jar-jar stood up. "What is my next assignment, my moronic little friend?" Jar-jar said nothing. "_What is my next assignment!_" he shrieked, his face inches from Jar-jar's. Jar-jar's mouth didn't twitch. Vader clenched his fist, Jar-jar grasped at his throat as he was hoisted into the air as the emperor watched in amusment, "Tell me what I want to know," he ignited his lightsaber, "and you might live to see your cell again." After a moment of silence Vader released him, ordering, "You _will _tell me about my next assignment."

Unfortunately Jar-jar's mind was not a strong one, "Meesa _will _tell you Ani." He said blissfully.

"You _will_ hit yourself if you call me that again."

"Meesa sorry, Vader sir. Aayla Secura going on topa secret mission for Sen-ator Bail Organa. She was not dead by yoosa boys!"

"Thank you Jar-jar," said the Emperor, "your services are no longer necessary."

"He is right, Jar-jar." Said Darth Vader plesantly, "Just in time for the party too!"

"Party Vader sir?"

"Oh yes," sneered Vader gleefully, "it's just over there. I think Boss Nasa is going to give you another promotion, but only if you get there quick!"

"I am coming Boss Nasa!" cried Jar-jar, leaping to his feet and running in the direction Darth Vader was pointing, and out of the window and down 700 stories to the pavement.

"You _will _get there quick." Laughed the Emperor, "Very well done Lord Vader, I am surprised. You know the parameters of your mission now, Lord Vader?"

"Yes my master, I will follow Aayla Secura and terminate her miserable exsistence."

"Captain Rex and the 501st Combat Regiment will go with you."

"I do not need anyone to help me on this one."

"But you _do_ Lord Vader," interrupted Palpatine, "you _failed_ me last time, it must _not _happen again, for your sake."

"Yes, my master."


End file.
